[phenixbb] den refinement
Jeff Headd
jjheadd at lbl.gov
Tue Jun 11 08:54:38 PDT 2013
Hi Andreas,
My guess is that you have main.simulated_annealing=True also active in your
parameter file. You need to set this to False, and then the refinement
should proceed.
Jeff
On Tue, Jun 11, 2013 at 11:44 AM, Andreas Förster <docandreas at gmail.com>wrote:
> Dear all,
>
> I'm trying to get DEN refinement going from the command line. The run
> aborts quickly with the following error in the log file:
>
> Sorry: Cartesian simulated annealing should not be turned on for DEN
> refinement. Annealing settings are controlled in the den parameter scope.
>
> The DEN scope in input.def looks like this:
>
> den {
> reference_file = den_ref_Jun.pdb
> gamma = 0.5
> kappa = 0.1
> weight = 30
> sigma = 0.44
> optimize = True
> opt_gamma_values = 0 0.2 0.4 0.6 0.8 1
> opt_weight_values = 3 10 30 100 300
> num_cycles = 12
> kappa_burn_in_cycles = 2
> bulk_solvent_and_scale = True
> refine_adp = True
> final_refinement_cycle = False
> verbose = False
> annealing_type = *torsion cartesian
> output_kinemage = False
> restraint_network {
> lower_distance_cutoff = 3
> upper_distance_cutoff = 15
> sequence_separation_low = 0
> sequence_separation_limit = 10
> exclude_hydrogens = True
> ndistance_ratio = 1
> export_den_pairs = False
> den_network_file = None
> }
>
> Annealing type is torsion from what I can tell. What am I doing wrong?
>
> (Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2)
>
>
> Thanks.
>
>
> Andreas
>
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
> http://www.msf.bio.ic.ac.uk
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>
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